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Started by upstream project "BIOFORMATS-test-repo" build number 248 originally caused by: Started by upstream project "Trigger" build number 272 originally caused by: Started by timer Running as SYSTEM Building remotely on docker (swarm) in workspace /home/omero/workspace/BIOFORMATS-test-folder@6 [BIOFORMATS-test-folder@6] $ /bin/bash -xe /tmp/jenkins9352086498563137495.sh + '[' mrc = slidebook ']' ++ date +%u + '[' 4 -le 1 ']' + sudo docker run --rm --name BIOFORMATS-test-folder_39048_merge_ci -v /uod/idr/repos/curated/mrc:/data -v /uod/idr-scratch/merge-ci/curated/mrc:/config snoopycrimecop/bioformats:merge_ci -Dtestng.memory=15g -Dtestng.threadCount=12 Buildfile: /bio-formats-build/bioformats/components/test-suite/build.xml [echo] isSnapshot = true init-title: [echo] ----------=========== bio-formats-testing-framework ===========---------- init-timestamp: init: copy-resources: compile: [resolver:resolve] Resolving artifacts compile-tests: [resolver:resolve] Resolving artifacts [javac] Compiling 1 source file to /bio-formats-build/bioformats/components/test-suite/test [javac] warning: [options] bootstrap class path not set in conjunction with -source 8 [javac] warning: [options] source value 8 is obsolete and will be removed in a future release [javac] warning: [options] target value 8 is obsolete and will be removed in a future release [javac] warning: [options] To suppress warnings about obsolete options, use -Xlint:-options. [javac] 4 warnings test-automated: [testng] Could not load field socket from SocketImpl: java.lang.NoSuchFieldException: socket [testng] Could not load field serverSocket from SocketImpl: java.lang.NoSuchFieldException: serverSocket [testng] File leak detector installed [testng] 01:17:15,551 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [stdout] [testng] 01:17:15,592 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender] [testng] 01:17:15,618 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [SIFT] [testng] 01:17:15,619 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.classic.sift.SiftingAppender] [testng] 01:17:15,627 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [loci.tests.testng] to DEBUG [testng] 01:17:15,627 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to INFO [testng] 01:17:15,627 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [SIFT] to Logger[ROOT] [testng] 01:17:15,628 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [stdout] to Logger[loci.tests.testng] [testng] 01:17:15,628 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@2d710f1a - End of configuration. [testng] 01:17:15,629 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@13fd2ccd - Registering current configuration as safe fallback point [testng] 01:17:15,629 |-INFO in ch.qos.logback.classic.util.ContextInitializer@b9b00e0 - ch.qos.logback.classic.util.DefaultJoranConfigurator.configure() call lasted 477 milliseconds. ExecutionStatus=DO_NOT_INVOKE_NEXT_IF_ANY [testng] [2024-11-07 01:17:15,645] [main] java.version = 21 [testng] 01:17:15,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-main] [testng] 01:17:15,649 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:15,693 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-main] - File property is set to [target/bio-formats-test-main-2024-11-07_01-17-15.log] [testng] 01:17:15,695 |-INFO in ch.qos.logback.core.sift.SiftProcessor@1b919693 - End of configuration. [testng] [2024-11-07 01:17:15,696] [main] testng.directory = /data [testng] [2024-11-07 01:17:15,697] [main] testng.configDirectory = /config [testng] [2024-11-07 01:17:15,706] [main] testng.multiplier = 1.0 [testng] [2024-11-07 01:17:15,706] [main] testng.in-memory = false [testng] [2024-11-07 01:17:15,706] [main] testng.allow-missing = false [testng] [2024-11-07 01:17:15,706] [main] user.language = en [testng] [2024-11-07 01:17:15,706] [main] user.country = ${user.country} [testng] [2024-11-07 01:17:15,706] [main] Maximum heap size = 15360 MB [testng] Scanning for files... [testng] [2024-11-07 01:17:22,631] [main] ---------------------------------------- [testng] [2024-11-07 01:17:22,631] [main] Total files: 20 [testng] [2024-11-07 01:17:22,631] [main] Scan time: 6.924 s (346 ms/file) [testng] [2024-11-07 01:17:22,632] [main] ---------------------------------------- [testng] Building list of tests... [testng] Ready to test 20 files [testng] [TestNG] Running: [testng] Bio-Formats software test suite [testng] [testng] [2024-11-07 01:17:28,676] [pool-1-thread-1] Initializing /data/jcb/thylakoid5.rec: [testng] 01:17:28,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-1] [testng] 01:17:28,676 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:28,677 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-1] - File property is set to [target/bio-formats-test-pool-1-thread-1-2024-11-07_01-17-28.log] [testng] 01:17:28,678 |-INFO in ch.qos.logback.core.sift.SiftProcessor@53b1bfbc - End of configuration. [testng] [2024-11-07 01:17:29,006] [pool-1-thread-12] Initializing /data/gh-3297/old-header/1160-no-endian-marker.mrc: [testng] 01:17:29,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-12] [testng] 01:17:29,007 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:29,007 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-12] - File property is set to [target/bio-formats-test-pool-1-thread-12-2024-11-07_01-17-29.log] [testng] 01:17:29,008 |-INFO in ch.qos.logback.core.sift.SiftProcessor@2875682b - End of configuration. [testng] [2024-11-07 01:17:29,323] [pool-1-thread-11] Initializing /data/public/EMDB/EMD-2225/EMD-2225.map: [testng] 01:17:29,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-11] [testng] 01:17:29,323 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:29,324 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-11] - File property is set to [target/bio-formats-test-pool-1-thread-11-2024-11-07_01-17-29.log] [testng] 01:17:29,324 |-INFO in ch.qos.logback.core.sift.SiftProcessor@44c9c346 - End of configuration. [testng] [2024-11-07 01:17:29,622] [pool-1-thread-10] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl_00002ef.mrc: [testng] 01:17:29,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-10] [testng] 01:17:29,623 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:29,625 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-10] - File property is set to [target/bio-formats-test-pool-1-thread-10-2024-11-07_01-17-29.log] [testng] 01:17:29,626 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3cce03c - End of configuration. [testng] [2024-11-07 01:17:30,179] [pool-1-thread-9] Initializing /data/strand/Series1_A.mrc: [testng] 01:17:30,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-9] [testng] 01:17:30,179 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,180 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-9] - File property is set to [target/bio-formats-test-pool-1-thread-9-2024-11-07_01-17-30.log] [testng] 01:17:30,180 |-INFO in ch.qos.logback.core.sift.SiftProcessor@f13b924 - End of configuration. [testng] [2024-11-07 01:17:30,521] [pool-1-thread-8] Initializing /data/ascb/c191ali.mrc: [testng] 01:17:30,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-8] [testng] 01:17:30,522 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,523 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-8] - File property is set to [target/bio-formats-test-pool-1-thread-8-2024-11-07_01-17-30.log] [testng] 01:17:30,524 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3e054f13 - End of configuration. [testng] [2024-11-07 01:17:30,908] [pool-1-thread-7] Initializing /data/ascb/cfa1071.mrc: [testng] 01:17:30,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-7] [testng] 01:17:30,908 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:30,909 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-7] - File property is set to [target/bio-formats-test-pool-1-thread-7-2024-11-07_01-17-30.log] [testng] 01:17:30,910 |-INFO in ch.qos.logback.core.sift.SiftProcessor@6be4386f - End of configuration. [testng] [2024-11-07 01:17:31,412] [pool-1-thread-6] Initializing /data/samples/1160.mrc: [testng] 01:17:31,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-6] [testng] 01:17:31,413 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:31,413 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-6] - File property is set to [target/bio-formats-test-pool-1-thread-6-2024-11-07_01-17-31.log] [testng] 01:17:31,414 |-INFO in ch.qos.logback.core.sift.SiftProcessor@788b2ea1 - End of configuration. [testng] [2024-11-07 01:17:31,671] [pool-1-thread-5] Initializing /data/will/CCDB-3587/wt_g21A2_bin3-ali.mrc: [testng] 01:17:31,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-5] [testng] 01:17:31,671 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:31,672 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-5] - File property is set to [target/bio-formats-test-pool-1-thread-5-2024-11-07_01-17-31.log] [testng] 01:17:31,672 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5e92f434 - End of configuration. [testng] [2024-11-07 01:17:31,901] [pool-1-thread-4] Initializing /data/dan/one.mrc: [testng] 01:17:31,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-4] [testng] 01:17:31,901 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:31,902 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-4] - File property is set to [target/bio-formats-test-pool-1-thread-4-2024-11-07_01-17-31.log] [testng] 01:17:31,903 |-INFO in ch.qos.logback.core.sift.SiftProcessor@5b60ca87 - End of configuration. [testng] [2024-11-07 01:17:32,221] [pool-1-thread-3] Initializing /data/samples/golgi.mrc: [testng] 01:17:32,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-3] [testng] 01:17:32,221 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:32,222 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-3] - File property is set to [target/bio-formats-test-pool-1-thread-3-2024-11-07_01-17-32.log] [testng] 01:17:32,222 |-INFO in ch.qos.logback.core.sift.SiftProcessor@3948f91c - End of configuration. [testng] [2024-11-07 01:17:32,601] [pool-1-thread-2] Initializing /data/dan/two.mrc: [testng] 01:17:32,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [logfile-pool-1-thread-2] [testng] 01:17:32,602 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [loci.tests.testng.TimestampedLogFileAppender] [testng] 01:17:32,603 |-INFO in loci.tests.testng.TimestampedLogFileAppender[logfile-pool-1-thread-2] - File property is set to [target/bio-formats-test-pool-1-thread-2-2024-11-07_01-17-32.log] [testng] 01:17:32,603 |-INFO in ch.qos.logback.core.sift.SiftProcessor@629bcc5b - End of configuration. [testng] [2024-11-07 01:17:38,069] [pool-1-thread-11] Initializing /data/will/AMI-public-data/GroEL/05may19a_00013gr_00008sq_00002hl.mrc: [testng] [2024-11-07 01:17:38,391] [pool-1-thread-3] Initializing /data/ticket-10073/wtjoin4.rec: [testng] [2024-11-07 01:17:38,648] [pool-1-thread-8] Initializing /data/bioformats2raw-198/test_uint8.mrc: [testng] [2024-11-07 01:17:38,912] [pool-1-thread-1] Initializing /data/samples/agar-exttype/golgi-modified-AGAR.mrc: [testng] [2024-11-07 01:17:39,196] [pool-1-thread-5] Initializing /data/ascb/c191.st: [testng] [2024-11-07 01:17:39,455] [pool-1-thread-10] Initializing /data/jcb/thyl-apr23-4.rec: [testng] [2024-11-07 01:17:39,771] [pool-1-thread-4] Initializing /data/ascb/514_9903.mrc: [testng] [2024-11-07 01:17:40,833] [pool-1-thread-2] Initializing /data/dan/three.mrc: [testng] [testng] =============================================== [testng] Bio-Formats software test suite [testng] Total tests run: 1060, Failures: 0, Skips: 0 [testng] =============================================== [testng] BUILD SUCCESSFUL Total time: 34 seconds Finished: SUCCESS